• Genomics & Informatics
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• v.16 no.4
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• pp.23.1-23.5
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• 2018

Virus taxonomy was initially determined by clinical experiments based on phenotype. However, with the development of sequence analysis methods, genotype-based classification was also applied. With the development of genome sequence analysis technology, there is an increasing demand for virus taxonomy to be extended from in vivo and in vitro to in silico. In this study, we verified the consistency of the current International Committee on Taxonomy of Viruses taxonomy using an in silico approach, aiming to identify the specific sequence for each virus. We applied this approach to norovirus in Caliciviridae, which causes 90% of gastroenteritis cases worldwide. First, based on the dogma "protein structure determines its function," we hypothesized that the specific sequence can be identified by the specific structure. Firstly, we extracted the coding region (CDS). Secondly, the CDS protein sequences of each genus were annotated by the conserved domain database (CDD) search. Finally, the conserved domains of each genus in Caliciviridae are classified by RPS-BLAST with CDD. The analysis result is that Caliciviridae has sequences including RNA helicase in common. In case of Norovirus, Calicivirus coat protein C terminal and viral polyprotein N-terminal appears as a specific domain in Caliciviridae. It does not include in the other genera in Caliciviridae. If this method is utilized to detect specific conserved domains, it can be used as classification keywords based on protein functional structure. After determining the specific protein domains, the specific protein domain sequences would be converted to gene sequences. This sequences would be re-used one of viral bio-marks.

• Korean journal of applied entomology
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• v.62 no.1
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• pp.49-56
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• 2023

We first report 4 unrecorded species belonging to genus Aleiodes Wesmael discovered in South Korea: A. lipwigi, A. guidaae, A. subemarginatus, A. caprinus. In this study, diagnosis, distribution, and illustration, DNA barcode sequence are provided for identification of these species.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2022.09a
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• pp.55-55
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• 2022

Corylopsis Siebold & Zucc. (Hamamelidaceae) is widely used for horticultural plant and comprise ca. 25 species in East Asia (1 species in Korea; 4 species in Japan; 20 species in China). Previous revisions have gone from 7 to more than 30 species, causing confusion in the nursery industry and public gardens. Due to morphological similarity within Corylopsis, molecular research is needed to distinguish it. In this study, the chloroplast genome of C. gotoana and C. pauciflora distributed in Japan was completed by using NGS (Next-Generation Sequencing) technique. The genome size of C. gotoana and C. pauciflora were 159,434 bp (large single-copy (LSC): 88,164 bp; small single-copy (SSC): 18,702 bp; inverted repeat regions (IRs): 26,284 bp) and 159,363 bp (LSC: 88,097 bp; SSC: 18,700 bp; IRs: 26,283 bp), respectively. In addition, we investigated the repeats, SNPs, and indels, and that could be used as DNA markers. Phylogenetic analysis demonstrated that C. pauciflora was sister to C. gotoana and C. spicata. The genus Corylopsis is a monophyletic group and Loropetalum is closely related to Corylopsis. The results of our study will provide the basic data necessary for the analysis of the species identification markers and genetic diversity within the genus Corylopsis in the future.

• Journal of Microbiology and Biotechnology
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• v.11 no.6
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• pp.1046-1054
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• 2001

Bioleaching is the process in which insoluble metal sulfide is oxidized by specialized iron- and/or sulfur-oxidizing lithotrophic bacteria in acidic, metal-rich environments. Most of these processes are carried out by the genus Thiobacillus. Three novel Thiobacillus strains (Thiobacillus thiooxidans AZ11, Thiobacillus thiooxidans MET, and thiobacillus thiooxidans TAS) associated with bioleaching have been isolated from soil and sludge (Korean patent No. 1999-0073060 for T. thiooxidans AZ11, Korean patent No. 1999-0005798 for T. thiooxidans MET, and Korean patent No. 1999-0073059 for T. thiooxidans TAS). A partial sequence of 16S ribosomal RNA gene (16S rDNA) and the entire sequence of 16S/23S intergenic spacer region (ISR) were determined in the three above novel strains and in Thiobacillus ferrooxidans ATCC19859 as a reference strain. When phylogenetic analysis was performed based on G+C contents and sequence alignments, T. ferroxidans ATCC19859 was found to be closely related to previously registered T. ferrooxidans strains in a monophyletic manner, while the three novel T. thiooxidans strains were classified in a paraphyletic manner. Close examination on the base composition of 16S/23S ISR revealed that the 5\` part (nucleotide residues 21-200) was specific for the genus Thiobacillus. On the other end, the 3\` part (nucleotide residues 201-520) showed specificity in T. ferrooxidans strains, but not in T. thiooxidans strains. These results suggest that the proximal and distal halves of 16S/23S could be used as a genetic marker for the identification of the genus Thiobacillus and the species T. ferrooxidans, respectively.

• Journal of Microbiology and Biotechnology
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• v.12 no.1
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• pp.176-181
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• 2002

In order to isolate and identify Bifidobacterium spp. that originated in Korea, feces were sampled from healthy Korean adults and children living in three villages, the first having a history of longevity and the other two where the diet did not include fermented milk or any pharmaceutical preparations. Through the use of Gram staining and microscopic examination for cell morphology, 23 bacterial strains presumed to be the Bifidobacterium genus were isolated from the feces of 13 out of a total of 59 Korean people. To identify the Bifidobacterium strains at the genus level, these bacteria were then analyzed by TLC and the fructose-6-phosphate phosphoketolase (F6PPK) test. The result showed that 22 of the isolated strains were confirmed to be members of the genus Bifidobacterium. All of these bifidobacteria were also identified as Bifidobacterium spp. by the fermentation test. Using a RFLP analysis, an attempt was made to identify the Bifidobacterium spp. that had been isolated from both Korean adults and children. In a genomic Southern blot analysis after digestion with two restriction enzymes (EcoRI, HindIII), all of the 14 randomly selected Korean isolates showed patterns identical to those of three different B. longum species. Another restriction enzyme, CfoI (4-bp recognition enzyme), was then used to identify the strain. Interestingly, all the Korean isolates were identified as B. longum ATCC 15708, indicating that a RFLP analysis was effective for identifying Bifidobacterium spp. at both the strain and species levels.

• Journal of the Korean Society of Tobacco Science
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• v.2 no.1
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• pp.17-27
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• 1980

From 143 sources of collected samples, the distribution of nicotinophiles were investigated and the biological characteristics as well as the rate of nicotine degradation were determined for the selected 34 strains which could grow successfully in the nicotine media, and one of the most effective strains was chosen and identified at the species level. Nicotinophils were distributed abundantly in the soils rich with organic materials, tobacco seed and root. The selected 34 strains were classified into 7 genus and identified with 4 strains of Arthrobacter, 11 strains of non-pigmented Pseudomonas, 2 strains of pigmented Pseudomonas, 6 strains of Alkaligenes, 5 strains Chromobacter 2 strains of Listeria and 4 strains of Achromobacter. Pseeudomonas and Alkaligenes were better than other genus in the rate of nicotine degradation and tobacco seed and root were also good sources for the isolation of effective nicotinophiles. Amnog 34 strains, strain NCT 27 which exhibited 97.l% of nicotine degradation rate was the best one for nicotine degradation and was indentified with Pseudomonas putida.

• The Plant Pathology Journal
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• v.32 no.6
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• pp.500-507
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• 2016

Single-molecule real-time (SMRT) sequencing allows identification of methylated DNA bases and methylation patterns/motifs at the genome level. Using SMRT sequencing, diverse bacterial methylomes including those of Helicobacter pylori, Lactobacillus spp., and Escherichia coli have been determined, and previously unreported DNA methylation motifs have been identified. However, the methylomes of Xanthomonas species, which belong to the most important plant pathogenic bacterial genus, have not been documented. Here, we report the methylomes of Xanthomonas axonopodis pv. glycines (Xag) strain 8ra and X. campestris pv. vesicatoria (Xcv) strain 85-10. We identified $N^6$-methyladenine (6mA) and $N^4$-methylcytosine (4mC) modification in both genomes. In addition, we assigned putative DNA methylation motifs including previously unreported methylation motifs via REBASE and MotifMaker, and compared methylation patterns in both species. Although Xag and Xcv belong to the same genus, their methylation patterns were dramatically different. The number of 4mC DNA bases in Xag (66,682) was significantly higher (29 fold) than in Xcv (2,321). In contrast, the number of 6mA DNA bases (4,147) in Xag was comparable to the number in Xcv (5,491). Strikingly, there were no common or shared motifs in the 10 most frequently methylated motifs of both strains, indicating they possess unique species- or strain-specific methylation motifs. Among the 20 most frequent motifs from both strains, for 9 motifs at least 1% of the methylated bases were located in putative promoter regions. Methylome analysis by SMRT sequencing technology is the first step toward understanding the biology and functions of DNA methylation in this genus.

• Korean Journal of Plant Resources
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• v.8 no.3
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• pp.303-318
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• 1995

Microscopic structures of epidermis and palynology and isozyme analysis were examined to find out the intergeneric and interspecific relationships and consequently to confirm the position of Hanabusaya aiatica as an endemic genus among 4 genera and 9 species belonging to the Hanabusaya asiatica, Korean endemic, and its allied groups. In the examination of microscopic structures of epidermis, cell patterns of perianth and ultrastructure of seed coat were found to be useful characters for the identification of the 4 genera and 9 species. Palynological characters such as microscopic structure and overall morphology of pollen grains were, however, not enough to distinguish them because of the great variabilities in these traits. Isozyme analysis showed that H. asiatica was very closly related to Campanula punctata and C. takesimana, though there were variations among populations and collected areas in some classified groups, depending on classified groups. Based on these results, the position of H. asiatica as an endemic genus was well confirmed.

• Korean Journal of Plant Resources
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• v.8 no.3
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• pp.223-235
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• 1995

Comparative studies on external morphology and anatomical characters were conducted understand the interspecific relationships and possibly to identify the position of Hanabusaya asiatica as an endemic genus among 4 genera and 9 species in H. asiatica and its allied groups. Such morphological characteristics as root shape, leaf size, presence or absence of wings in petiole, corolla and calyx shape, and inflorescence and stigma shape were useful qualitative characters. The morphology of stem, peduncle, calyx lobe, leaf, petiole, and ovary were also good characters to be included in this identification study. In the anatomical observations in these organs, projecting degree of epidermis and number of projecting area rather than cross-sectioned internal structures were found to be valuable index for the classification among species. External morphology and anatomical characters support the position of H. asiatica as an endemic genus very well. Known as the most important external characters to taxonomists(Fedorov, 1957: Nakai, 1952: Hong, 1983), leaf arrangement, inflorescence, and corolla shape were also preven to be very useful characters to identify the genera and species in the H. asiatica and its allied groups.

• Animal cells and systems
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• v.4 no.1
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• pp.1-7
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• 2000

The genus Dendronephthya, generally known as soft corals, is reported as an abundant and variable taxon. They mostly distribute in warmer waters of the Undo-Pacific Ocean region including Korea. In spite of their abundance and ecological importance as habitats of marine organisms, there are difficulties in the study of their identification and systematics because they have morphological variabilities and limited taxonomec characters. To resolve the problems, we attempted to elucidate the genetic relationships in the genus Dendronephthya by using random amplified polymorphic DNA (RAPD) analysis. This study was based on eight dendronephthian species and one Alcyoniidae species, Alcyonium gracillimum, as an outgroup. The results from all analysis suggest that they could be classified into four groups by the growth form and the anthocodial grades as follows: the first one,D. putteri and D. suensoni with the divaricate form and VI grade; the second one,D. sp.1 and D. sp.2 with the divaricate form and III or IV grade; the third one, D. gigantea and D. aurea being closer than D. spinifera with the glomerate form and III grade; the last one, D. castanea related to D. gigantea rather than D. putteri with the umbellate form and IV grade. Moreover, the divaricate form was separated from the group of the glomerate and umbellate form. At the intraspecies level, the types of the D. castanea, D. gigantea and D. spinifera were separated depending on the feature of spicules in the polyp head, and the coloration could not influence genetic variation. From this study, we can confirm that their morphological characters are compatible with the genetic variation, also RAPD analysis is a very useful method for resolving the systematic relationships of den-deonephthians.